The funding structure is on a five year rolling system, designed to allow the Council and its secretariat some flexibility to plan future work while maintaining intellectual independence and giving adequate financial stability.

Occasionally, the Council also receives funds for specific projects: for example, in 2004 the Medical Research Council, the Wellcome Trust, the UK Department for International Development and the Rockefeller Foundation provided funding for a workshop on the ethics of healthcare research in developing countries; and in 2010 the Nuffield Foundation and the Arts and Humanities Research Council agreed to jointly fund a Council-based Fellowship on solidarity.